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Yorodumi- PDB-4pzp: Substrate-free structure of D-alanine carrier protein ligase DltA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pzp | ||||||
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Title | Substrate-free structure of D-alanine carrier protein ligase DltA from Bacillus cereus | ||||||
Components | D-alanine--poly(phosphoribitol) ligase subunit 1 | ||||||
Keywords | LIGASE / Homologous to acetyl-coA synthetase | ||||||
Function / homology | Function and homology information D-alanine-[D-alanyl-carrier protein] ligase / D-alanine [D-alanyl carrier protein] ligase activity / lipoteichoic acid biosynthetic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus cereus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Du, L. / Atila, M. / Luo, Y. | ||||||
Citation | Journal: F1000Res / Year: 2014 Title: Thiolation-enhanced substrate recognition by D-alanyl carrier protein ligase DltA from Bacillus cereus. Authors: Du, L. / Luo, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pzp.cif.gz | 110 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pzp.ent.gz | 82.6 KB | Display | PDB format |
PDBx/mmJSON format | 4pzp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pzp_validation.pdf.gz | 427.4 KB | Display | wwPDB validaton report |
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Full document | 4pzp_full_validation.pdf.gz | 440.1 KB | Display | |
Data in XML | 4pzp_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 4pzp_validation.cif.gz | 31.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/4pzp ftp://data.pdbj.org/pub/pdb/validation_reports/pz/4pzp | HTTPS FTP |
-Related structure data
Related structure data | 3dhvS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Monomer |
-Components
#1: Protein | Mass: 57565.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579 / DSM 31 / Gene: BC_1372, dltA / Plasmid: pet28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q81G39, EC: 6.1.1.13 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.94 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 0.1 M MgCl2,0.5 M KCl, 0.05 M HEPES-NAOH buffer, 16% 3350 , pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: Brukers Proteum / Detector: CCD / Date: Apr 26, 2008 / Details: mirrors |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→33.1 Å / Num. all: 37973 / Num. obs: 32733 / % possible obs: 86.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 7.53 |
Reflection shell | Resolution: 1.9→2 Å / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.321 / % possible all: 37.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3DHV Resolution: 1.9→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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